There’s bad news and good news about Honolulu’s rail transit system.

First, the bad news: There’s less money than anticipated, and needed modifications will result in higher costs.

Now, the good news: The federal commitment remains strong and the modifications will improve the safety and convenience of the rail system for commuters.

The Obama administration has called for a full $250 million next year, but federal sequestration will take a $14 million bite out of anticipated funding this year, according to Dan Grabauskas, CEO of the Honolulu Authority for Rapid Transportation (HART).

The reduction is "one we can absolutely live with in terms of cash flow this year," he said, noting that the federal government is committed to $1.55 billion total for rail through 2019.

Even so, there’s more money available that the city should receive. The state continues to collect 10 percent of the 0.5 percent general excise tax surcharge for rail levied on Oahu residents. The state’s 10 percent skim resulted in $35 million in the final two quarters of last year, more than enough to cover the state Tax Department’s entire budget.

The state should provide an explanation to the city, and return every penny that’s not needed for the administrative cost of collecting the surcharge.

A state Supreme Court ruling halted construction of the rail system last August until HART completed an archaeological survey along the 20-mile, 21-stop route between east Kapolei and Ala Moana. Sixteen columns had been set and about 50 additional column foundations had been completed in West Oahu.

HART has now completed that survey and promised to move or otherwise protect the seven human remains that were found from 260 trenches.

"I’ve come to believe we can have a project that is respectful to the past but also able to move forward to serve the people in the future, and that’s what we’re trying to do," Grabauskas told the Star-Advertiser’s editorial board last week.

With that archaeological survey completed, it’s hoped that the work stoppage will be lifted, allowing construction in Kapolei to resume by the end of September and reach downtown in mid-2014.

HART also has complied with a federal judge’s order to meet three conditions to supplement a federal environmental impact statement about the rail line’s effect, including on historic Mother Waldron Park in Kakaako and on cultural areas in the city center. These reports, recently finished, are being reviewed by the Federal Transit Administration.

Meanwhile, rail cars are being changed with more seats than initially ordered, with each two-car train including 96 seats instead of 76.

Oahu taxpayers best brace themselves — again — for another upcoming change order for a design element that was drawn on plans but inexplicably, left out of budgeting. Grabaus-kas has proposed an important improvement for stations, where commuters will board the trains. He wants "platform screen gates," with doors to separate the commuter from the open track, and which open only when the train pulls up.

It is "absolutely the most safe thing to do," he said.

He also makes sense in calling for fare gates, with passengers using a "smart card" to gain entrance to the train at stations, preventing them from hopping over turnstiles or entering at open entrances. In other rail systems, revenues improved by as much as 10 percent when such systems were replaced with fare gates.

At some point, the city must decide whether management of the rail and bus systems should be consolidated under one authority. It’s a proposal worth considering. Rail and bus must work seamlessly together to provide maximum coverage efficiently. A single authority for a relatively small system like Oahu’s should make more sense than two parallel administrative agencies.

The bottom line, as Grabauskas points out, is an integrated transit system that appears seamless to the customer — one that is "reliable, on time, easy to use," with one customer service number and one website. That, and keeping the rail project on track, on budget and on schedule for its 2019 completion date.

This badly needed expansion of Oahu’s public transportation system is long overdue.